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Install Packages
#install packages
install.packages("BiocManager")Error in install.packages : Updating loaded packagesinstall.packages("forcats")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forcats_1.0.0.tar.gz'
Content type 'application/x-gzip' length 294183 bytes (287 KB)
==================================================
downloaded 287 KB
* installing *source* package ‘forcats’ ...
** package ‘forcats’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (forcats)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("stringr")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.5.0.tar.gz'
Content type 'application/x-gzip' length 175699 bytes (171 KB)
==================================================
downloaded 171 KB
* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (stringr)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("BiocManager")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.20.tar.gz'
Content type 'application/x-gzip' length 265248 bytes (259 KB)
==================================================
downloaded 259 KB
* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("ggplot2")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.4.1.tar.gz'
Content type 'application/x-gzip' length 3150856 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggplot2)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("ggrepel")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/ggrepel_0.9.3.tar.gz'
Content type 'application/x-gzip' length 136189 bytes (132 KB)
==================================================
downloaded 132 KB
* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** using staged installation
** libsg++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c repel_boxes.cpp -o repel_boxes.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ggrepel.so RcppExports.o repel_boxes.o -L/usr/lib/R/lib -lRinstalling to /home/mouse/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ggrepel/00new/ggrepel/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggrepel)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("readr")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/readr_2.1.4.tar.gz'
Content type 'application/x-gzip' length 298083 bytes (291 KB)
==================================================
downloaded 291 KB
* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** using staged installation
** libsg++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Collector.cpp -o Collector.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CollectorGuess.cpp -o CollectorGuess.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Iconv.cpp -o Iconv.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c LocaleInfo.cpp -o LocaleInfo.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Reader.cpp -o Reader.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Source.cpp -o Source.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Tokenizer.cpp -o Tokenizer.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c TokenizerDelim.cpp -o TokenizerDelim.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c TokenizerFwf.cpp -o TokenizerFwf.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c TokenizerWs.cpp -o TokenizerWs.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c connection.cpp -o connection.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c datetime.cpp -o datetime.o
gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c grisu3.c -o grisu3.o
gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c parse.cpp -o parse.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read.cpp -o read.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c type_convert.cpp -o type_convert.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write.cpp -o write.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write_delim.cpp -o write_delim.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o cpp11.o datetime.o grisu3.o init.o parse.o read.o type_convert.o write.o write_delim.o -L/usr/lib/R/lib -lRinstalling to /home/mouse/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-readr/00new/readr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (readr)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("tidyr")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/tidyr_1.3.0.tar.gz'
Content type 'application/x-gzip' length 823546 bytes (804 KB)
==================================================
downloaded 804 KB
* installing *source* package ‘tidyr’ ...
** package ‘tidyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libsg++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c melt.cpp -o melt.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simplifyPieces.cpp -o simplifyPieces.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tidyr.so cpp11.o melt.o simplifyPieces.o -L/usr/lib/R/lib -lRinstalling to /home/mouse/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-tidyr/00new/tidyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tidyr)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’install.packages("survminer")Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/survminer_0.4.9.tar.gz'
Content type 'application/x-gzip' length 3599577 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
* installing *source* package ‘survminer’ ...
** package ‘survminer’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survminer)
The downloaded source packages are in
‘/tmp/RtmpVpfP8o/downloaded_packages’BiocManager::install("GEOquery")'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'GEOquery'Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, foreign, Matrix, spatialBiocManager::install("limma")'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'limma'Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, foreign, Matrix, spatialBiocManager::install("pheatmap")'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'pheatmap'Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, foreign, Matrix, spatialBiocManager::install("org.Hs.eg.db")'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'org.Hs.eg.db'Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, foreign, Matrix, spatialImporting the data. The function to download a GEO data-set is getGEO from GEOquery package.
library(GEOquery)Registered S3 method overwritten by 'data.table':
method from
print.data.table
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)#Passive smoker dataset
my_idPS <- "GSE18044"
#Active Smoker Data set
my_idAS <- "GSE27272"
gsePS <- getGEO(my_idPS)Found 1 file(s)
GSE18044_series_matrix.txt.gzgseAS <- getGEO(my_idAS)Found 1 file(s)
GSE27272_series_matrix.txt.gzSome data-sets on GEO may be derived from different micro-array platforms. Therefore the object gse is a list of different data-sets. You can find out how many were used by checking the length of the gse object. Usually there will only be one platform and the dataset we want to analyse will be the first object in the list (gse[[1]]). If more than one dataset is present, you can analyse the other dataset by changing the number inside the [[…]] ## e.g. gse <- galse[[2]] Check how many platforms used
print(length(gsePS))[1] 1print(length(gseAS))[1] 1gsePS <- gsePS[[1]]
gsePSExpressionSet (storageMode: lockedEnvironment)
assayData: 11155 features, 76 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM451162 GSM451163 ... GSM451237 (76 total)
varLabels: title geo_accession ... status:ch1 (46 total)
varMetadata: labelDescription
featureData
featureNames: ILMN_1343291 ILMN_1343292 ... ILMN_2038778 (11155 total)
fvarLabels: ID Species ... GB_ACC (26 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 20092892
Annotation: GPL6104 gseAS <- gseAS[[1]]Check the normalisation and scales used. For visualization and statistical analysis, we will inspect the data to discover what scale the data are presented in. The methods we will use assume the data are on a log2 scale; typically in the range of 0 to 16. The exprs function can retrieve the expression values as a data frame; with one column per-sample and one row per-gene.
#Passive Smoking Dataset
pData(gsePS) ## print the sample informationfData(gsePS) ## print the gene annotationexprs(gsePS) ## print the expression data GSM451162 GSM451163 GSM451164 GSM451165 GSM451166 GSM451167 GSM451168 GSM451169 GSM451170 GSM451171 GSM451172 GSM451173
ILMN_1343291 149.38 161.57 155.86 155.13 130.20 153.16 170.44 205.75 145.86 153.64 181.06 116.34
ILMN_1343292 149.38 161.57 155.86 155.13 130.20 153.16 170.44 205.75 145.86 153.64 181.06 116.34
ILMN_1343293 259.05 329.22 301.73 247.79 270.24 256.82 253.69 265.28 273.89 296.67 283.68 289.36
ILMN_1343294 69.95 96.98 81.77 67.75 77.58 69.91 70.34 69.59 73.38 73.37 82.37 84.03
ILMN_1651228 248.58 159.55 140.13 197.94 222.67 202.40 207.33 217.45 388.62 148.81 206.83 225.91
ILMN_1651229 960.18 915.18 982.76 1005.17 866.05 862.65 815.36 1006.45 801.85 856.01 1052.66 965.98
ILMN_1651237 185.23 200.89 227.25 181.25 197.69 224.51 254.41 204.17 188.95 228.36 236.14 225.36
ILMN_1651254 154.86 114.90 135.19 124.11 146.09 121.58 175.21 150.20 154.52 153.35 193.97 134.58
ILMN_1651261 248.58 159.55 140.13 197.94 222.67 202.40 207.33 217.17 388.62 148.81 206.83 225.91
ILMN_1651262 291.69 264.66 216.53 357.54 241.07 215.51 238.92 243.78 322.73 259.96 317.24 236.14
ILMN_1651268 117.79 82.40 70.78 83.01 104.68 79.18 73.33 80.09 85.31 98.57 104.95 67.06
ILMN_1651278 75.19 67.51 71.18 67.60 85.05 74.53 74.08 76.30 88.51 62.36 71.45 104.04
ILMN_1651282 1523.99 1370.75 1335.80 1648.18 1622.62 1805.98 1427.94 1414.23 1530.31 1356.39 1712.23 2297.66
GSM451174 GSM451175 GSM451176 GSM451177 GSM451178 GSM451179 GSM451180 GSM451181 GSM451182 GSM451183 GSM451184 GSM451185
ILMN_1343291 135.82 140.63 122.72 140.27 117.25 126.55 124.66 159.02 109.61 116.45 148.11 120.12
ILMN_1343292 135.82 140.63 122.72 140.27 117.25 126.55 124.66 159.02 109.61 116.45 148.11 120.12
ILMN_1343293 287.91 280.99 268.45 269.44 244.39 286.78 294.58 250.08 190.45 208.14 272.25 229.67
ILMN_1343294 76.84 70.19 80.26 72.89 74.00 73.37 65.88 67.17 65.31 68.03 69.50 70.74
ILMN_1651228 199.70 207.73 363.54 68.43 145.88 251.22 121.05 127.00 354.33 359.75 224.58 1542.59
ILMN_1651229 771.40 992.70 770.97 1036.26 937.96 944.27 991.32 940.97 965.40 863.47 863.47 778.51
ILMN_1651237 204.28 190.76 230.32 223.87 227.74 197.19 208.40 191.11 215.24 184.17 223.37 144.75
ILMN_1651254 150.85 147.90 123.81 154.14 165.56 146.48 189.02 181.22 138.54 141.18 143.26 132.81
ILMN_1651261 199.70 207.73 363.54 68.43 145.88 251.22 121.05 127.00 354.33 359.75 224.58 1542.59
ILMN_1651262 242.66 235.72 212.60 249.40 284.87 231.42 219.94 237.46 226.53 336.14 277.44 256.00
ILMN_1651268 82.46 91.38 69.36 90.63 89.68 70.87 92.52 85.28 64.79 77.59 65.14 79.42
ILMN_1651278 67.96 111.17 153.81 72.99 78.09 92.07 77.04 90.11 95.19 125.62 87.57 149.12
ILMN_1651282 2487.78 1693.46 1606.46 2421.18 2157.73 2091.75 2232.53 1735.75 2029.32 1800.43 1918.57 1599.61
GSM451186 GSM451187 GSM451188 GSM451189 GSM451190 GSM451191 GSM451192 GSM451193 GSM451194 GSM451195 GSM451196 GSM451197
ILMN_1343291 156.25 130.79 139.19 144.70 137.22 151.76 147.32 153.94 139.27 159.41 108.50 151.16
ILMN_1343292 156.25 130.79 139.19 144.70 137.22 151.76 147.32 153.94 139.27 159.41 108.50 151.16
ILMN_1343293 304.11 307.44 267.39 218.56 221.34 219.72 200.32 251.69 338.29 276.62 281.33 292.23
ILMN_1343294 94.36 69.99 76.94 64.30 69.60 76.86 68.53 66.73 62.16 73.80 61.24 59.93
ILMN_1651228 1195.60 130.15 173.01 350.58 287.11 347.81 371.58 180.17 314.99 232.66 455.84 449.19
ILMN_1651229 779.19 917.32 974.50 873.58 956.78 867.57 869.03 1165.13 1258.45 1274.96 986.63 1092.54
ILMN_1651237 251.59 171.58 187.96 106.05 197.40 189.40 175.45 195.37 191.11 172.60 183.90 173.19
ILMN_1651254 155.63 157.59 144.40 160.57 151.16 161.28 173.93 153.81 195.43 167.58 129.82 152.75
ILMN_1651261 1195.60 130.15 173.01 350.58 287.11 347.81 371.58 180.17 314.99 232.66 455.84 449.19
ILMN_1651262 349.59 263.48 209.32 273.57 243.55 324.79 347.75 337.86 317.51 279.44 203.24 232.98
ILMN_1651268 72.61 101.26 76.68 78.39 79.23 70.24 103.81 71.88 61.26 71.64 94.84 70.55
ILMN_1651278 75.06 71.40 64.27 190.19 99.86 87.91 107.76 72.39 84.04 109.42 171.98 110.81
ILMN_1651282 1728.11 1999.94 1834.85 1984.98 1977.11 1400.14 1387.58 1837.92 2128.59 2075.09 1604.80 1855.47
GSM451198 GSM451199 GSM451200 GSM451201 GSM451202 GSM451203 GSM451204 GSM451205 GSM451206 GSM451207 GSM451208 GSM451209
ILMN_1343291 147.38 161.12 166.02 168.01 160.30 139.11 132.07 137.01 151.44 164.30 149.34 157.78
ILMN_1343292 147.38 161.12 166.02 168.01 160.30 139.11 132.09 137.01 151.44 164.30 149.34 157.78
ILMN_1343293 296.03 270.73 283.56 278.87 333.26 296.95 292.98 279.34 260.53 287.62 279.80 313.08
ILMN_1343294 64.49 63.07 66.50 61.48 107.64 67.25 69.91 65.36 68.40 72.00 63.73 72.41
ILMN_1651228 225.16 272.52 230.20 495.25 201.48 222.82 146.20 124.65 121.05 127.70 187.07 218.86
ILMN_1651229 1215.38 1272.01 1087.24 1266.36 753.72 930.65 860.29 768.61 925.23 943.73 851.13 900.15
ILMN_1651237 168.08 197.10 202.14 197.00 370.68 207.11 228.77 235.38 210.31 204.11 201.96 249.48
ILMN_1651254 167.86 191.29 148.40 165.71 135.94 132.41 134.63 135.28 194.71 174.99 150.75 175.39
ILMN_1651261 225.16 272.52 230.20 495.25 201.48 222.82 146.20 124.65 121.05 127.70 187.07 218.86
ILMN_1651262 235.83 258.79 276.86 269.67 252.64 225.04 280.99 192.83 197.66 254.87 194.78 234.34
ILMN_1651268 78.00 76.42 86.98 76.58 89.30 80.25 79.68 97.89 93.44 92.36 119.44 76.82
ILMN_1651278 118.11 107.63 98.88 148.79 76.67 89.43 104.57 72.99 76.64 103.82 72.09 85.16
ILMN_1651282 1809.03 2052.69 1974.94 1984.98 2173.90 1882.37 1900.94 1895.74 1518.89 1786.33 2086.73 2349.43
GSM451210 GSM451211 GSM451212 GSM451213 GSM451214 GSM451215 GSM451216 GSM451217 GSM451218 GSM451219 GSM451220 GSM451221
ILMN_1343291 146.32 142.71 161.47 161.04 126.72 123.00 131.73 129.45 133.47 110.47 123.37 130.42
ILMN_1343292 146.32 142.71 161.47 161.04 126.72 123.00 131.73 129.45 133.47 110.47 123.37 130.42
ILMN_1343293 259.75 301.47 275.13 271.46 317.13 353.46 277.20 325.55 284.58 285.70 304.98 268.93
ILMN_1343294 73.82 73.29 65.64 72.57 74.63 72.87 85.44 83.64 86.72 71.58 69.31 82.14
ILMN_1651228 149.12 163.43 187.04 181.56 183.11 128.64 176.55 173.69 181.72 316.84 214.82 317.88
ILMN_1651229 1036.26 976.27 947.96 818.85 785.34 853.16 1023.08 951.63 709.39 856.48 846.67 932.35
ILMN_1651237 197.86 246.81 206.54 212.77 215.84 241.99 229.71 173.89 242.95 195.11 219.29 222.61
ILMN_1651254 152.10 151.04 144.70 169.72 167.76 165.94 169.19 159.90 184.89 151.28 143.96 180.83
ILMN_1651261 149.12 163.43 187.04 181.56 183.11 128.64 176.55 173.69 181.72 316.84 214.82 317.88
ILMN_1651262 225.23 284.67 308.46 293.74 228.57 194.03 237.91 254.24 374.52 233.38 417.27 320.19
ILMN_1651268 70.81 95.76 98.75 113.96 84.27 96.77 88.99 82.36 106.70 79.84 75.28 72.26
ILMN_1651278 74.18 77.68 87.89 97.07 86.83 74.37 88.05 69.56 90.29 93.03 111.52 95.70
ILMN_1651282 1791.96 1589.11 1774.30 1986.91 1734.38 1740.44 2562.24 1530.31 2777.14 3040.15 2661.15 3014.13
GSM451222 GSM451223 GSM451224 GSM451225 GSM451226 GSM451227 GSM451228 GSM451229 GSM451230 GSM451231 GSM451232 GSM451233
ILMN_1343291 110.82 133.47 143.52 160.43 114.30 135.46 135.32 116.77 149.54 133.37 116.89 155.58
ILMN_1343292 110.82 133.47 143.52 160.43 114.30 135.46 135.32 116.77 149.54 133.37 116.89 155.58
ILMN_1343293 347.62 308.29 311.82 250.61 259.55 286.43 315.32 297.58 302.15 255.02 263.61 222.09
ILMN_1343294 72.95 75.68 79.60 72.81 70.85 73.16 66.48 61.71 64.67 72.42 73.10 99.75
ILMN_1651228 191.79 215.68 176.57 415.25 232.48 277.88 191.16 642.24 163.56 204.14 557.54 160.19
ILMN_1651229 981.69 956.78 792.59 650.33 849.36 976.77 710.40 904.32 920.72 770.56 867.57 747.52
ILMN_1651237 223.62 221.63 269.82 266.07 232.10 219.53 202.89 174.61 256.04 224.39 212.60 249.18
ILMN_1651254 157.89 155.43 119.27 145.17 153.11 140.87 177.77 123.45 148.04 117.62 148.07 178.35
ILMN_1651261 191.79 215.68 176.57 415.25 232.48 277.60 191.16 642.24 163.56 204.14 557.54 160.19
ILMN_1651262 240.49 240.42 253.80 252.57 277.25 262.93 291.16 185.23 248.27 261.61 235.65 230.46
ILMN_1651268 113.01 74.35 75.08 97.79 76.40 73.67 86.96 97.11 91.36 82.64 92.61 87.65
ILMN_1651278 124.06 98.24 79.69 101.65 77.93 78.36 78.55 132.41 84.85 104.32 145.57 93.07
ILMN_1651282 1678.74 1912.49 2225.04 1999.94 3136.89 2819.87 2633.90 1981.30 1938.51 2251.87 1805.98 1851.97
GSM451234 GSM451235 GSM451236 GSM451237
ILMN_1343291 167.81 138.51 140.73 161.17
ILMN_1343292 167.81 138.51 140.73 161.17
ILMN_1343293 269.17 261.87 286.33 304.17
ILMN_1343294 85.17 84.89 81.15 85.68
ILMN_1651228 228.39 178.70 151.41 218.93
ILMN_1651229 821.36 699.58 674.15 953.21
ILMN_1651237 209.50 229.44 225.64 229.54
ILMN_1651254 152.45 146.86 150.57 155.82
ILMN_1651261 228.39 178.70 151.12 218.93
ILMN_1651262 255.80 236.14 254.53 271.65
ILMN_1651268 100.19 94.44 92.06 75.02
ILMN_1651278 81.73 79.83 77.63 82.86
ILMN_1651282 2167.65 2077.36 2077.36 2440.48
[ reached getOption("max.print") -- omitted 11142 rows ]#Active Smoking Dataset
pData(gseAS) ## print the sample informationfData(gseAS) ## print the gene annotationexprs(gseAS) ## print the expression data GSM674181 GSM674182 GSM674183 GSM674184 GSM674185 GSM674186 GSM674187 GSM674188 GSM674189 GSM674190 GSM674191
ILMN_1343291 14.8619778 14.7910049 14.7452011 14.7910049 14.8619778 14.7452011 14.8619778 14.6982075 14.7452011 14.7910049 14.7452011
ILMN_1651209 2.5685167 2.7272693 2.7475569 2.6750045 2.5532888 3.3415974 2.4195101 2.6927972 2.7817207 2.2441842 3.2584289
ILMN_1651228 8.5750943 9.9841923 10.3281227 9.8260592 10.0326597 9.0887247 10.8615345 11.3055992 10.0466991 10.5095958 10.3484435
ILMN_1651229 3.1590667 4.1096401 4.5489735 5.2069581 5.0817526 4.4604426 4.1898441 4.2047952 4.5915581 4.4294000 4.3272872
ILMN_1651235 1.7496571 2.1460404 1.9005771 2.3356164 2.0435947 1.9749846 2.3473446 2.4599578 1.9248186 1.9696352 1.8733256
GSM674192 GSM674193 GSM674194 GSM674195 GSM674196 GSM674197 GSM674198 GSM674199 GSM674200 GSM674201 GSM674202
ILMN_1343291 14.3158285 14.5259423 14.7910049 14.8619778 14.6982075 14.4652898 14.5764206 14.4869054 14.8619778 14.7452011 14.7910049
ILMN_1651209 3.3729830 2.7147483 2.9519653 2.5016719 2.0643223 2.7545884 2.5575992 2.5980040 2.0244837 2.5827687 2.8940409
ILMN_1651228 10.0200275 9.8842667 10.7143717 10.6503148 10.2273249 9.9799361 10.1677480 9.9179893 10.6673446 10.3621971 11.4263771
ILMN_1651229 4.0406611 3.8099323 4.5554201 4.6069612 4.0509786 3.8099323 4.5118417 4.2672160 4.5021940 4.1772376 3.4124302
ILMN_1651235 1.8907805 1.8003602 2.0608954 2.3280294 1.9153709 2.4077274 1.9532964 1.7104076 2.0458226 2.0820828 1.6283743
GSM674203 GSM674204 GSM674205 GSM674206 GSM674207 GSM674208 GSM674209 GSM674210 GSM674211 GSM674212 GSM674213
ILMN_1343291 14.1302842 14.3464777 14.3653147 14.5499591 14.6651862 14.1758769 14.7452011 14.5499591 14.5499591 14.6982075 14.6319381
ILMN_1651209 2.1543775 3.3384963 2.7121567 2.0215363 2.3192907 2.0602498 2.6337253 2.9488517 2.2383876 2.4524280 2.2789914
ILMN_1651228 10.5980718 10.1702768 9.8600703 10.9399263 11.4553938 10.0200275 9.3211019 10.2602759 10.0662662 11.3539900 11.3594342
ILMN_1651229 4.1671320 3.8671932 3.0109870 4.0086356 3.7742856 2.7045066 3.2348003 4.7926620 3.8676837 4.2365312 4.5941497
ILMN_1651235 1.5184042 1.6027677 1.7192858 2.7088267 1.5315885 2.2193393 3.0533658 2.1313841 1.6761320 1.9036561 1.6141945
GSM674214 GSM674215 GSM674216 GSM674217 GSM674218 GSM674219 GSM674220 GSM674221 GSM674222 GSM674223 GSM674224
ILMN_1343291 14.8619778 14.8619778 14.2060070 14.7910049 14.7910049 14.8619778 14.7910049 14.7910049 14.5259423 14.3464777 14.6027668
ILMN_1651209 2.7800397 3.2371026 2.9539295 2.9357204 3.2459192 2.2769161 2.8643361 2.3292605 3.0322662 1.7062384 1.4615467
ILMN_1651228 11.3262496 11.0983170 11.2868194 11.6558441 11.2092185 10.5909254 11.7766805 11.6396209 11.7184957 10.0888207 10.3388581
ILMN_1651229 4.8008259 4.9267999 5.2674562 4.0155367 3.9691965 4.7323616 4.8451105 3.8914343 4.6388481 2.6981938 3.2076198
ILMN_1651235 1.4401514 1.3687787 2.1066137 1.6991814 2.7388188 1.0317704 1.9215757 1.5905028 1.7750802 1.5192519 2.4095676
GSM674225 GSM674226 GSM674227 GSM674228 GSM674229 GSM674230 GSM674231 GSM674232 GSM674233 GSM674234 GSM674235
ILMN_1343291 14.7452011 14.6027668 14.7910049 14.7452011 14.4869054 14.7452011 14.6982075 14.5077111 14.7910049 14.5259423 14.7910049
ILMN_1651209 2.4205234 2.2272267 2.7582861 2.9662652 2.1270319 3.1211454 3.4732736 2.7209212 1.5670327 2.5166910 2.8136225
ILMN_1651228 10.5737572 10.3586630 11.2746011 11.2092185 10.6336150 10.7897432 11.2018201 11.1907319 11.6487341 11.0501232 11.8929778
ILMN_1651229 5.5282177 4.6904697 3.1992837 3.7780043 3.6389730 4.6250598 3.8518855 4.5914539 4.0730380 4.0356761 4.6148738
ILMN_1651235 2.0107251 2.0951334 2.0884350 2.2512684 2.4399999 1.7953190 2.0742323 1.6963980 1.4932238 1.6530551 1.7861499
GSM674236 GSM674237 GSM674238 GSM674239 GSM674240 GSM674241 GSM674242 GSM674243 GSM674244 GSM674245 GSM674282
ILMN_1343291 14.6651862 14.2209468 14.8619778 14.4002420 14.8619778 14.5077111 14.3464777 14.7910049 14.7452011 14.7452011 14.8669818
ILMN_1651209 2.6695269 3.5877183 2.6066791 1.9514989 1.9204960 2.1210264 2.5852612 1.3731196 3.0567458 3.0996575 2.8597060
ILMN_1651228 11.7156361 10.0649749 11.1792289 10.5115523 9.8454368 10.6162368 9.8474156 9.5614657 10.3972041 10.0738616 9.2438970
ILMN_1651229 4.2121943 4.4693053 4.2804220 4.4299211 4.5281000 4.6050552 5.3613444 1.8589038 5.0375551 4.8153558 6.5884598
ILMN_1651235 2.6358671 2.0348639 2.2910378 1.7740890 1.8108544 2.7827124 2.3606424 1.7602213 1.8334249 1.6556977 1.5598855
GSM674283 GSM674284 GSM674285 GSM674286 GSM674287 GSM674288 GSM674289 GSM674290 GSM674291 GSM674292 GSM674293
ILMN_1343291 14.2970073 14.8669818 14.5485991 14.5846971 14.7446305 14.3937962 14.7446305 14.6776908 14.6300193 14.5846971 14.7446305
ILMN_1651209 2.7866525 2.2942225 3.4518428 2.6782817 2.6545643 2.5303211 2.8669747 2.6842813 3.5076923 2.5966956 2.2604187
ILMN_1651228 9.1212002 9.3065155 9.2038637 9.2365503 9.7389173 9.5730171 9.1671784 9.3560903 9.0109836 9.0606835 9.9839853
ILMN_1651229 5.5479582 6.2473030 6.3915213 5.6875967 6.2941456 6.8176207 6.1565746 6.3307417 6.2914905 6.8543444 6.5645643
ILMN_1651235 2.2866530 2.1405070 2.1935872 1.5613664 1.7418406 2.2222765 1.6514138 1.9616269 1.9590055 2.1656142 1.9890106
GSM674294 GSM674295 GSM674296 GSM674297 GSM674298 GSM674299 GSM674300 GSM674301 GSM674302 GSM674303 GSM674304
ILMN_1343291 14.6776908 14.4514737 14.8669818 14.8669818 14.8669818 14.6300193 14.6776908 14.6300193 14.6300193 14.6300193 14.6776908
ILMN_1651209 2.4525984 3.2438927 1.8431472 2.1567333 2.0214230 3.3123641 2.1837161 1.9289795 2.3012542 2.2347472 2.7080298
ILMN_1651228 9.7595112 9.8516618 11.1372391 11.3671765 11.2337077 9.8965737 10.4857861 10.9318827 10.7136345 10.1932937 9.9702953
ILMN_1651229 6.3579337 7.5810176 5.5306939 6.5132096 6.2658574 6.9405233 6.4635283 6.3134180 6.2585382 6.5671119 6.0563209
ILMN_1651235 2.2772461 2.0772998 1.6588625 1.5962859 1.5520857 2.4321910 2.1481835 2.2113218 1.8018961 2.4649837 2.6024249
GSM674305 GSM674306 GSM674307 GSM674308 GSM674309 GSM674310 GSM674311 GSM674312 GSM674313 GSM674314 GSM674315
ILMN_1343291 14.7446305 14.7446305 14.8669818 14.5846971 14.5485991 14.7446305 14.7446305 13.8342572 14.4514737 14.5485991 14.6776908
ILMN_1651209 2.1609801 1.5426242 2.4050770 3.1014624 2.1299504 2.6088141 1.4429639 3.3283915 2.2741790 1.4744680 2.1483135
ILMN_1651228 10.7783201 11.5179215 10.4411918 10.8776186 9.9227118 10.6815714 10.9839949 11.4211297 11.2639495 10.7601360 11.4019354
ILMN_1651229 6.1015973 6.2117883 6.1875568 6.3610525 6.5339310 5.9402849 6.3048743 7.6011659 7.1978414 6.6393796 6.6255985
ILMN_1651235 1.6621861 2.0765158 1.5297423 2.6610012 1.5736676 1.6086295 2.6409783 1.5370337 1.9262640 1.5446570 1.5507172
GSM674316 GSM674317 GSM674318 GSM674319 GSM674320 GSM674321 GSM674322 GSM674323 GSM674324 GSM674325 GSM674326
ILMN_1343291 14.5846971 14.6776908 14.8669818 14.2540347 14.6776908 14.6300193 14.7446305 14.6776908 14.7446305 14.7446305 14.7446305
ILMN_1651209 2.3542759 2.5987051 2.4038210 3.2799448 3.3749177 2.7413456 2.8334551 2.9769641 1.8607884 2.0665267 2.2579338
ILMN_1651228 11.4507248 11.5553999 11.1253792 11.0279854 10.9890261 9.6940703 10.6254560 10.4638658 10.9291390 10.6254560 11.0316789
ILMN_1651229 6.1597562 7.0322198 5.9334322 7.3975591 6.9196361 6.7909868 6.8018210 6.2873643 6.1433642 6.2455196 5.9799070
ILMN_1651235 1.8525512 1.7992732 2.1137866 1.8829099 2.0555567 2.2086053 2.0375019 1.7909797 1.2741860 1.7572010 2.0349234
GSM674327 GSM674328 GSM674329 GSM674330 GSM674331 GSM674332 GSM674333 GSM674334 GSM674335 GSM674344 GSM674345
ILMN_1343291 14.5485991 14.7446305 14.6776908 14.6776908 14.5485991 14.6300193 14.7446305 14.6776908 14.6300193 14.5381996 14.5780819
ILMN_1651209 2.4705036 2.3918427 2.0012014 1.9239242 2.1022741 2.2996707 2.9240841 2.9832345 2.4272538 1.8354051 2.8784357
ILMN_1651228 10.3563497 10.3221160 10.2452752 9.6459614 10.8800591 10.5515619 10.9005339 10.4876663 10.4465277 10.1531222 10.6507552
ILMN_1651229 5.9342262 6.8321071 6.7018967 5.7886166 5.7147863 5.2385398 5.7172206 5.5381003 6.3433512 4.1053476 5.1837752
ILMN_1651235 2.1994342 1.8815883 2.0649804 1.8985712 1.2508803 2.2151086 2.5775372 1.6296972 1.8795056 1.6792910 2.3277708
GSM674346 GSM674347 GSM674348 GSM674349 GSM674350 GSM674351 GSM674352 GSM674353 GSM674354 GSM674355 GSM674356
ILMN_1343291 14.6763922 14.5381996 14.5381996 14.7432068 14.6763922 14.6763922 14.6763922 14.6763922 14.7432068 14.6205539 14.5780819
ILMN_1651209 3.0699665 3.3623307 3.0952438 2.7826015 3.1019396 2.3953646 3.1841707 2.3882802 2.1021650 3.4607306 3.1439099
ILMN_1651228 10.5703830 10.1575640 9.3771117 10.7811385 10.8424860 10.8424860 10.9626655 10.2534790 11.3199148 11.4385430 11.1683191
ILMN_1651229 4.6612206 4.8930973 5.0399211 5.2358327 4.6213188 4.7000349 4.6655129 4.5665047 4.6386040 5.5381361 4.5019196
ILMN_1651235 2.4591110 1.7208283 1.7852430 1.8534349 1.9293621 1.6148108 2.0706519 2.1453816 1.6197573 1.9987733 1.8334965
GSM674357 GSM674358 GSM674359 GSM674360 GSM674361 GSM674362 GSM674363 GSM674364 GSM674365 GSM674366 GSM674367
ILMN_1343291 14.5100191 14.6763922 14.6763922 14.5780819 14.6763922 14.9304275 14.9304275 14.7432068 14.9304275 14.4750391 14.5100191
ILMN_1651209 2.6166347 2.5778365 2.9148343 3.3618320 3.7071059 2.4489487 2.5592007 4.0001492 2.8624496 2.7744766 1.8177584
ILMN_1651228 11.3729133 11.2800181 10.6453119 11.1308828 10.7372395 11.4162806 11.4347151 11.2240437 10.9346891 12.2331067 11.9884317
ILMN_1651229 4.6205709 5.7863155 4.4170681 4.9141539 4.8756530 3.6233818 4.3721628 5.8038052 4.7446543 5.0825770 5.5475251
ILMN_1651235 1.9391840 1.6764801 1.6000156 1.5291720 2.7411907 3.2669709 2.2647482 3.5263763 2.1603423 1.6808062 2.0878640
GSM674368 GSM674369 GSM674370 GSM674371 GSM674372 GSM674373 GSM674374 GSM674375 GSM674376 GSM674377 GSM674378
ILMN_1343291 14.9304275 14.7432068 14.5381996 14.9304275 14.6763922 14.6205539 14.5381996 14.7432068 14.7432068 14.7432068 14.7432068
ILMN_1651209 3.6543929 2.9524580 2.4085480 2.5198109 3.3497347 3.0028326 2.9638433 3.1105393 3.6443485 2.7389128 3.4080067
ILMN_1651228 11.8933188 11.9587291 12.1378779 11.3982976 11.2240437 10.0595683 10.7086102 11.7148977 11.7682867 11.4497738 11.1627601
ILMN_1651229 5.0648312 4.9738923 5.1901189 4.7324017 4.9295341 5.3648923 5.4440649 5.4742133 5.7344326 5.5969800 5.2254154
ILMN_1651235 1.7133883 2.1495297 1.3106208 2.1421694 2.0203264 2.0501583 1.8027632 2.1474522 1.5732898 2.1181844 2.0708921
GSM674379 GSM674380 GSM674381 GSM674382 GSM674383 GSM674384 GSM674385 GSM674386 GSM674387 GSM674388 GSM674389
ILMN_1343291 14.6205539 14.6763922 14.6763922 14.5780819 14.7432068 14.7432068 14.7432068 14.7432068 14.4131767 14.9304275 14.6205539
ILMN_1651209 2.4236271 2.8614553 2.8988961 3.0119205 3.0141082 3.0583510 2.1811141 2.9350100 2.4008032 2.3358918 2.8239546
ILMN_1651228 11.8504341 11.5707499 11.6264803 12.0488571 11.4310339 11.2800181 10.3702607 10.9626655 11.5541332 10.6322653 10.9612812
ILMN_1651229 5.9543351 5.9582613 5.1454887 5.9337991 4.2399777 5.7353076 4.7147375 6.2045911 5.6519743 5.0966169 5.3418335
ILMN_1651235 1.7872678 2.2265947 1.6255226 2.1713515 2.8554764 1.9505383 2.0039577 1.6785918 1.5637831 1.6518372 1.4480261
GSM674390 GSM674391 GSM674392 GSM674393 GSM674394 GSM674395 GSM674396 GSM674397 GSM674398 GSM674399 GSM674400
ILMN_1343291 14.6205539 14.6205539 14.7432068 14.7432068 14.7432068 14.7432068 14.6763922 14.7432068 14.6763922 14.7432068 14.7432068
ILMN_1651209 3.2664697 2.8730511 2.3035390 2.6139301 4.2937556 3.2158692 3.6507478 2.0020956 2.2201926 3.0632576 3.2441759
ILMN_1651228 11.3630119 11.9404693 11.4454111 10.8329959 10.6136104 10.5212532 10.7275257 11.0056648 10.3258850 10.5761667 10.6782012
ILMN_1651229 5.6196229 6.5421974 4.6741590 5.0555842 5.4242350 5.1598772 5.7181292 5.0241896 5.4880515 6.3289077 4.4259048
ILMN_1651235 2.1484274 2.2507025 2.3818827 1.7530639 1.8777645 1.8637018 1.7980119 1.9933630 1.9427921 1.8303903 1.9530155
GSM674401 GSM674402 GSM674403 GSM674404 GSM674405 GSM674406 GSM674407
ILMN_1343291 14.7432068 14.7432068 14.6763922 14.7432068 14.7432068 14.7432068 14.7432068
ILMN_1651209 3.3487016 3.4401422 2.2405803 3.2349158 2.2318294 1.9505383 2.3713452
ILMN_1651228 10.5435433 10.6369493 11.4602394 10.7513246 10.6525819 11.4057107 11.7872534
ILMN_1651229 5.2381301 4.6090295 3.6550872 5.7181292 5.6076725 5.3782176 6.0621664
ILMN_1651235 1.3498251 1.9116361 1.9097331 2.4694678 1.8778786 1.3277622 1.3969692
[ reached getOption("max.print") -- omitted 24521 rows ]The summary function can then be used to print the distributions.
## exprs get the expression levels as a data frame and get the distribution
summary(exprs(gsePS)) GSM451162 GSM451163 GSM451164 GSM451165 GSM451166 GSM451167 GSM451168
Min. : 69.95 Min. : 67.51 Min. : 70.78 Min. : 67.6 Min. : 70.18 Min. : 69.91 Min. : 70.34
1st Qu.: 117.79 1st Qu.: 103.96 1st Qu.: 98.88 1st Qu.: 100.1 1st Qu.: 93.77 1st Qu.: 101.57 1st Qu.: 105.22
Median : 214.33 Median : 200.89 Median : 211.24 Median : 197.9 Median : 181.96 Median : 215.51 Median : 207.33
Mean : 644.97 Mean : 564.37 Mean : 604.19 Mean : 651.3 Mean : 589.80 Mean : 641.00 Mean : 607.12
3rd Qu.: 431.17 3rd Qu.: 376.59 3rd Qu.: 362.47 3rd Qu.: 455.1 3rd Qu.: 409.92 3rd Qu.: 484.91 3rd Qu.: 438.07
Max. :4577.08 Max. :4188.76 Max. :4302.45 Max. :4397.3 Max. :3648.54 Max. :3957.03 Max. :3854.98
GSM451169 GSM451170 GSM451171 GSM451172 GSM451173 GSM451174 GSM451175
Min. : 69.59 Min. : 62.87 Min. : 62.36 Min. : 71.45 Min. : 61.34 Min. : 65.06 Min. : 70.19
1st Qu.: 105.92 1st Qu.: 91.64 1st Qu.: 99.31 1st Qu.: 116.12 1st Qu.: 104.04 1st Qu.: 101.23 1st Qu.: 101.18
Median : 217.10 Median : 246.73 Median : 226.75 Median : 233.95 Median : 225.36 Median : 204.28 Median : 182.75
Mean : 576.58 Mean : 628.23 Mean : 545.69 Mean : 663.25 Mean : 699.44 Mean : 663.20 Mean : 639.25
3rd Qu.: 371.72 3rd Qu.: 416.42 3rd Qu.: 403.28 3rd Qu.: 361.16 3rd Qu.: 455.31 3rd Qu.: 390.17 3rd Qu.: 809.12
Max. :4029.33 Max. :4037.12 Max. :3304.50 Max. :4749.54 Max. :4250.30 Max. :4311.29 Max. :4176.00
GSM451176 GSM451177 GSM451178 GSM451179 GSM451180 GSM451181 GSM451182
Min. : 69.36 Min. : 67.49 Min. : 65.97 Min. : 66.92 Min. : 65.88 Min. : 67.17 Min. : 64.79
1st Qu.: 99.88 1st Qu.: 90.63 1st Qu.: 89.68 1st Qu.: 98.80 1st Qu.: 92.52 1st Qu.: 93.57 1st Qu.: 95.19
Median : 229.15 Median : 189.11 Median : 227.74 Median : 231.42 Median : 199.26 Median : 191.11 Median : 195.49
Mean : 660.73 Mean : 676.09 Mean : 690.10 Mean : 685.89 Mean : 665.28 Mean : 624.51 Mean : 631.34
3rd Qu.: 469.75 3rd Qu.: 476.25 3rd Qu.: 444.14 3rd Qu.: 403.84 3rd Qu.: 490.42 3rd Qu.: 484.70 3rd Qu.: 411.67
Max. :3994.13 Max. :4219.00 Max. :4198.77 Max. :4188.76 Max. :4188.76 Max. :3656.17 Max. :3490.05
GSM451183 GSM451184 GSM451185 GSM451186 GSM451187 GSM451188 GSM451189
Min. : 61.36 Min. : 65.14 Min. : 66.22 Min. : 66.51 Min. : 69.99 Min. : 64.27 Min. : 64.1
1st Qu.: 114.59 1st Qu.: 98.75 1st Qu.: 117.43 1st Qu.: 99.41 1st Qu.: 104.40 1st Qu.: 95.78 1st Qu.: 106.0
Median : 184.17 Median : 224.58 Median : 209.70 Median : 241.14 Median : 171.58 Median : 190.03 Median : 214.8
Mean : 656.13 Mean : 693.17 Mean : 680.92 Mean : 636.53 Mean : 609.69 Mean : 677.53 Mean : 666.9
3rd Qu.: 559.41 3rd Qu.: 463.03 3rd Qu.: 778.51 3rd Qu.: 779.19 3rd Qu.: 509.14 3rd Qu.: 433.82 3rd Qu.: 403.4
Max. :4291.82 Max. :4749.54 Max. :4188.76 Max. :3535.39 Max. :3870.51 Max. :4924.12 Max. :4291.8
GSM451190 GSM451191 GSM451192 GSM451193 GSM451194 GSM451195 GSM451196
Min. : 69.60 Min. : 70.24 Min. : 68.53 Min. : 66.73 Min. : 61.26 Min. : 61.30 Min. : 53.27
1st Qu.: 99.86 1st Qu.: 111.26 1st Qu.: 107.76 1st Qu.: 84.42 1st Qu.: 102.55 1st Qu.: 98.72 1st Qu.: 94.84
Median : 221.34 Median : 219.72 Median : 253.14 Median : 195.37 Median : 220.49 Median : 232.66 Median : 203.67
Mean : 638.54 Mean : 618.70 Mean : 587.92 Mean : 701.29 Mean : 710.22 Mean : 712.88 Mean : 565.86
3rd Qu.: 467.60 3rd Qu.: 495.56 3rd Qu.: 554.95 3rd Qu.: 590.93 3rd Qu.: 583.57 3rd Qu.: 585.55 3rd Qu.: 455.84
Max. :3725.19 Max. :3921.81 Max. :3200.93 Max. :4749.54 Max. :5142.26 Max. :4773.32 Max. :3040.15
GSM451197 GSM451198 GSM451199 GSM451200 GSM451201 GSM451202 GSM451203
Min. : 59.1 Min. : 61.68 Min. : 63.07 Min. : 66.50 Min. : 61.48 Min. : 75.92 Min. : 67.25
1st Qu.: 110.8 1st Qu.: 118.11 1st Qu.: 107.69 1st Qu.: 98.88 1st Qu.: 148.79 1st Qu.: 107.64 1st Qu.: 95.67
Median : 233.0 Median : 235.83 Median : 238.38 Median : 230.20 Median : 251.14 Median : 232.94 Median : 222.82
Mean : 688.6 Mean : 741.01 Mean : 700.92 Mean : 688.22 Mean : 722.32 Mean : 634.33 Mean : 598.12
3rd Qu.: 506.3 3rd Qu.: 634.35 3rd Qu.: 548.01 3rd Qu.: 553.47 3rd Qu.: 575.77 3rd Qu.: 407.12 3rd Qu.: 430.02
Max. :5158.4 Max. :5508.95 Max. :4761.82 Max. :4590.00 Max. :4938.49 Max. :3520.58 Max. :3273.86
GSM451204 GSM451205 GSM451206 GSM451207 GSM451208 GSM451209 GSM451210
Min. : 68.75 Min. : 65.36 Min. : 62.60 Min. : 72.0 Min. : 63.73 Min. : 60.82 Min. : 70.81
1st Qu.: 104.57 1st Qu.: 108.83 1st Qu.: 93.74 1st Qu.: 103.8 1st Qu.: 106.05 1st Qu.: 98.42 1st Qu.: 90.03
Median : 224.58 Median : 192.83 Median : 197.66 Median : 204.1 Median : 194.78 Median : 218.86 Median : 197.86
Mean : 599.24 Mean : 591.81 Mean : 585.37 Mean : 586.9 Mean : 606.90 Mean : 671.52 Mean : 611.38
3rd Qu.: 426.03 3rd Qu.: 438.07 3rd Qu.: 500.13 3rd Qu.: 434.5 3rd Qu.: 412.50 3rd Qu.: 398.99 3rd Qu.: 433.24
Max. :3804.90 Max. :3563.62 Max. :3297.63 Max. :3490.1 Max. :3448.61 Max. :4076.08 Max. :3628.08
GSM451211 GSM451212 GSM451213 GSM451214 GSM451215 GSM451216 GSM451217
Min. : 73.29 Min. : 63.02 Min. : 57.33 Min. : 70.57 Min. : 72.87 Min. : 67.06 Min. : 65.61
1st Qu.: 95.76 1st Qu.: 98.75 1st Qu.: 108.16 1st Qu.: 100.78 1st Qu.: 90.17 1st Qu.: 88.54 1st Qu.: 99.49
Median : 212.77 Median : 206.51 Median : 212.77 Median : 215.84 Median : 194.03 Median : 210.41 Median : 187.98
Mean : 567.80 Mean : 605.02 Mean : 604.00 Mean : 640.74 Mean : 612.08 Mean : 633.44 Mean : 580.17
3rd Qu.: 413.64 3rd Qu.: 474.43 3rd Qu.: 469.95 3rd Qu.: 447.11 3rd Qu.: 453.41 3rd Qu.: 392.24 3rd Qu.: 414.13
Max. :3252.03 Max. :3498.98 Max. :3436.55 Max. :3930.29 Max. :3741.04 Max. :3614.88 Max. :3443.62
GSM451218 GSM451219 GSM451220 GSM451221 GSM451222 GSM451223 GSM451224
Min. : 62.19 Min. : 71.58 Min. : 62.11 Min. : 72.26 Min. : 59.93 Min. : 66.73 Min. : 75.08
1st Qu.: 104.74 1st Qu.: 101.94 1st Qu.: 111.52 1st Qu.: 98.96 1st Qu.: 110.82 1st Qu.: 116.42 1st Qu.: 95.86
Median : 184.89 Median : 233.38 Median : 219.29 Median : 268.93 Median : 169.99 Median : 221.63 Median : 253.80
Mean : 695.01 Mean : 681.32 Mean : 682.65 Mean : 762.76 Mean : 613.57 Mean : 673.24 Mean : 672.81
3rd Qu.: 454.08 3rd Qu.: 444.60 3rd Qu.: 417.72 3rd Qu.: 425.01 3rd Qu.: 688.76 3rd Qu.: 450.34 3rd Qu.: 485.91
Max. :4837.99 Max. :4094.56 Max. :3974.74 Max. :5108.48 Max. :3475.10 Max. :3887.32 Max. :3887.32
GSM451225 GSM451226 GSM451227 GSM451228 GSM451229 GSM451230 GSM451231
Min. : 58.24 Min. : 69.74 Min. : 67.13 Min. : 58.13 Min. : 59.55 Min. : 63.16 Min. : 68.70
1st Qu.: 101.65 1st Qu.: 89.91 1st Qu.: 100.29 1st Qu.: 94.86 1st Qu.: 97.11 1st Qu.: 92.31 1st Qu.: 95.22
Median : 250.61 Median : 232.48 Median : 262.93 Median : 202.89 Median : 185.23 Median : 163.56 Median : 204.14
Mean : 617.60 Mean : 701.49 Mean : 703.98 Mean : 668.20 Mean : 645.63 Mean : 640.65 Mean : 618.18
3rd Qu.: 482.18 3rd Qu.: 592.00 3rd Qu.: 498.59 3rd Qu.: 493.10 3rd Qu.: 642.24 3rd Qu.: 479.84 3rd Qu.: 435.79
Max. :3634.31 Max. :3732.93 Max. :3870.51 Max. :3648.54 Max. :3570.66 Max. :4047.49 Max. :3605.82
GSM451232 GSM451233 GSM451234 GSM451235 GSM451236 GSM451237
Min. : 56.71 Min. : 72.40 Min. : 59.27 Min. : 51.17 Min. : 73.63 Min. : 63.67
1st Qu.: 103.03 1st Qu.: 99.75 1st Qu.: 117.73 1st Qu.: 104.55 1st Qu.: 91.22 1st Qu.: 92.15
Median : 213.68 Median : 178.35 Median : 209.50 Median : 201.05 Median : 177.11 Median : 218.93
Mean : 625.45 Mean : 591.06 Mean : 643.75 Mean : 604.08 Mean : 570.28 Mean : 624.31
3rd Qu.: 557.54 3rd Qu.: 416.27 3rd Qu.: 434.62 3rd Qu.: 396.64 3rd Qu.: 413.88 3rd Qu.: 415.70
Max. :3732.93 Max. :3382.05 Max. :4163.00 Max. :4057.80 Max. :3291.24 Max. :3831.09 summary(exprs(gseAS)) GSM674181 GSM674182 GSM674183 GSM674184 GSM674185 GSM674186 GSM674187
Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8251 1st Qu.: 1.8245 1st Qu.: 1.8257 1st Qu.: 1.8219 1st Qu.: 1.8270 1st Qu.: 1.8291 1st Qu.: 1.8257
Median : 2.9376 Median : 2.9407 Median : 2.9384 Median : 2.9367 Median : 2.9384 Median : 2.9366 Median : 2.9398
Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1472 3rd Qu.: 6.1475 3rd Qu.: 6.1470 3rd Qu.: 6.1470 3rd Qu.: 6.1476 3rd Qu.: 6.1467 3rd Qu.: 6.1471
GSM674188 GSM674189 GSM674190 GSM674191 GSM674192 GSM674193 GSM674194
Min. : 0.5453 Min. : 0.5453 Min. : 0.5718 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8199 1st Qu.: 1.8218 1st Qu.: 1.8303 1st Qu.: 1.8240 1st Qu.: 1.8229 1st Qu.: 1.8241 1st Qu.: 1.8258
Median : 2.9376 Median : 2.9331 Median : 2.9410 Median : 2.9398 Median : 2.9390 Median : 2.9375 Median : 2.9375
Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1617 Mean : 4.1617 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1475 3rd Qu.: 6.1472 3rd Qu.: 6.1467 3rd Qu.: 6.1467 3rd Qu.: 6.1472 3rd Qu.: 6.1461 3rd Qu.: 6.1471
GSM674195 GSM674196 GSM674197 GSM674198 GSM674199 GSM674200 GSM674201
Min. : 0.5453 Min. : 0.5453 Min. : 0.5718 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8234 1st Qu.: 1.8266 1st Qu.: 1.8257 1st Qu.: 1.8270 1st Qu.: 1.8278 1st Qu.: 1.8276 1st Qu.: 1.8251
Median : 2.9398 Median : 2.9390 Median : 2.9385 Median : 2.9395 Median : 2.9321 Median : 2.9392 Median : 2.9414
Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1617 Mean : 4.1618
3rd Qu.: 6.1467 3rd Qu.: 6.1472 3rd Qu.: 6.1470 3rd Qu.: 6.1474 3rd Qu.: 6.1472 3rd Qu.: 6.1471 3rd Qu.: 6.1464
GSM674202 GSM674203 GSM674204 GSM674205 GSM674206 GSM674207 GSM674208
Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5718 Min. : 0.5453
1st Qu.: 1.8238 1st Qu.: 1.8246 1st Qu.: 1.8246 1st Qu.: 1.8251 1st Qu.: 1.8217 1st Qu.: 1.8258 1st Qu.: 1.8258
Median : 2.9331 Median : 2.9335 Median : 2.9410 Median : 2.9376 Median : 2.9338 Median : 2.9374 Median : 2.9400
Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1616 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1465 3rd Qu.: 6.1475 3rd Qu.: 6.1475 3rd Qu.: 6.1470 3rd Qu.: 6.1464 3rd Qu.: 6.1467 3rd Qu.: 6.1453
GSM674209 GSM674210 GSM674211 GSM674212 GSM674213 GSM674214 GSM674215
Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8254 1st Qu.: 1.8250 1st Qu.: 1.8288 1st Qu.: 1.8278 1st Qu.: 1.8253 1st Qu.: 1.8275 1st Qu.: 1.8288
Median : 2.9387 Median : 2.9376 Median : 2.9411 Median : 2.9365 Median : 2.9373 Median : 2.9377 Median : 2.9396
Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1486 3rd Qu.: 6.1472 3rd Qu.: 6.1475 3rd Qu.: 6.1472 3rd Qu.: 6.1467 3rd Qu.: 6.1470 3rd Qu.: 6.1467
GSM674216 GSM674217 GSM674218 GSM674219 GSM674220 GSM674221 GSM674222
Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8218 1st Qu.: 1.8285 1st Qu.: 1.8187 1st Qu.: 1.8225 1st Qu.: 1.8270 1st Qu.: 1.8230 1st Qu.: 1.8312
Median : 2.9305 Median : 2.9357 Median : 2.9446 Median : 2.9376 Median : 2.9361 Median : 2.9375 Median : 2.9364
Mean : 4.1618 Mean : 4.1618 Mean : 4.1617 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1478 3rd Qu.: 6.1470 3rd Qu.: 6.1480 3rd Qu.: 6.1472 3rd Qu.: 6.1467 3rd Qu.: 6.1471 3rd Qu.: 6.1478
GSM674223 GSM674224 GSM674225 GSM674226 GSM674227 GSM674228 GSM674229
Min. : 0.5718 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8200 1st Qu.: 1.8316 1st Qu.: 1.8258 1st Qu.: 1.8344 1st Qu.: 1.8212 1st Qu.: 1.8203 1st Qu.: 1.8218
Median : 2.9396 Median : 2.9355 Median : 2.9329 Median : 2.9474 Median : 2.9355 Median : 2.9292 Median : 2.9454
Mean : 4.1617 Mean : 4.1617 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1479 3rd Qu.: 6.1450 3rd Qu.: 6.1467 3rd Qu.: 6.1470 3rd Qu.: 6.1461 3rd Qu.: 6.1450 3rd Qu.: 6.1475
GSM674230 GSM674231 GSM674232 GSM674233 GSM674234 GSM674235 GSM674236
Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8251 1st Qu.: 1.8305 1st Qu.: 1.8223 1st Qu.: 1.8200 1st Qu.: 1.8266 1st Qu.: 1.8305 1st Qu.: 1.8218
Median : 2.9375 Median : 2.9462 Median : 2.9298 Median : 2.9413 Median : 2.9305 Median : 2.9411 Median : 2.9387
Mean : 4.1615 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618
3rd Qu.: 6.1478 3rd Qu.: 6.1476 3rd Qu.: 6.1472 3rd Qu.: 6.1470 3rd Qu.: 6.1470 3rd Qu.: 6.1472 3rd Qu.: 6.1480
GSM674237 GSM674238 GSM674239 GSM674240 GSM674241 GSM674242 GSM674243
Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453 Min. : 0.5453
1st Qu.: 1.8258 1st Qu.: 1.8200 1st Qu.: 1.8200 1st Qu.: 1.8266 1st Qu.: 1.8266 1st Qu.: 1.8305 1st Qu.: 1.8212
Median : 2.9409 Median : 2.9297 Median : 2.9392 Median : 2.9344 Median : 2.9364 Median : 2.9439 Median : 2.9285
Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1618 Mean : 4.1617
3rd Qu.: 6.1467 3rd Qu.: 6.1472 3rd Qu.: 6.1470 3rd Qu.: 6.1467 3rd Qu.: 6.1475 3rd Qu.: 6.1472 3rd Qu.: 6.1480
GSM674244 GSM674245 GSM674282 GSM674283 GSM674284 GSM674285 GSM674286
Min. : 0.5453 Min. : 0.5453 Min. : 0.5107 Min. : 0.5107 Min. : 0.5395 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8224 1st Qu.: 1.8217 1st Qu.: 1.8407 1st Qu.: 1.8439 1st Qu.: 1.8418 1st Qu.: 1.8390 1st Qu.: 1.8381
Median : 2.9457 Median : 2.9305 Median : 3.1571 Median : 3.1558 Median : 3.1559 Median : 3.1539 Median : 3.1579
Mean : 4.1618 Mean : 4.1618 Mean : 4.2616 Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617
3rd Qu.: 6.1472 3rd Qu.: 6.1471 3rd Qu.: 6.3833 3rd Qu.: 6.3834 3rd Qu.: 6.3837 3rd Qu.: 6.3832 3rd Qu.: 6.3832
GSM674287 GSM674288 GSM674289 GSM674290 GSM674291 GSM674292 GSM674293
Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8372 1st Qu.: 1.8444 1st Qu.: 1.8407 1st Qu.: 1.8400 1st Qu.: 1.8445 1st Qu.: 1.8384 1st Qu.: 1.8431
Median : 3.1560 Median : 3.1559 Median : 3.1520 Median : 3.1573 Median : 3.1583 Median : 3.1517 Median : 3.1578
Mean : 4.2617 Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616
3rd Qu.: 6.3837 3rd Qu.: 6.3835 3rd Qu.: 6.3838 3rd Qu.: 6.3832 3rd Qu.: 6.3832 3rd Qu.: 6.3837 3rd Qu.: 6.3839
GSM674294 GSM674295 GSM674296 GSM674297 GSM674298 GSM674299 GSM674300
Min. : 0.5107 Min. : 0.5395 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8481 1st Qu.: 1.8400 1st Qu.: 1.8431 1st Qu.: 1.8445 1st Qu.: 1.8445 1st Qu.: 1.8405 1st Qu.: 1.8393
Median : 3.1521 Median : 3.1572 Median : 3.1557 Median : 3.1573 Median : 3.1562 Median : 3.1558 Median : 3.1572
Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616 Mean : 4.2616 Mean : 4.2616 Mean : 4.2616
3rd Qu.: 6.3837 3rd Qu.: 6.3832 3rd Qu.: 6.3837 3rd Qu.: 6.3834 3rd Qu.: 6.3830 3rd Qu.: 6.3837 3rd Qu.: 6.3835
GSM674301 GSM674302 GSM674303 GSM674304 GSM674305 GSM674306 GSM674307
Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8462 1st Qu.: 1.8441 1st Qu.: 1.8362 1st Qu.: 1.8405 1st Qu.: 1.8400 1st Qu.: 1.8431 1st Qu.: 1.8445
Median : 3.1574 Median : 3.1522 Median : 3.1629 Median : 3.1505 Median : 3.1579 Median : 3.1523 Median : 3.1562
Mean : 4.2616 Mean : 4.2616 Mean : 4.2616 Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616
3rd Qu.: 6.3840 3rd Qu.: 6.3830 3rd Qu.: 6.3834 3rd Qu.: 6.3846 3rd Qu.: 6.3821 3rd Qu.: 6.3832 3rd Qu.: 6.3840
GSM674308 GSM674309 GSM674310 GSM674311 GSM674312 GSM674313 GSM674314
Min. : 0.5107 Min. : 0.5107 Min. : 0.5395 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5395
1st Qu.: 1.8385 1st Qu.: 1.8393 1st Qu.: 1.8361 1st Qu.: 1.8441 1st Qu.: 1.8489 1st Qu.: 1.8484 1st Qu.: 1.8413
Median : 3.1521 Median : 3.1559 Median : 3.1559 Median : 3.1539 Median : 3.1573 Median : 3.1591 Median : 3.1557
Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616 Mean : 4.2616 Mean : 4.2616 Mean : 4.2616
3rd Qu.: 6.3821 3rd Qu.: 6.3832 3rd Qu.: 6.3834 3rd Qu.: 6.3832 3rd Qu.: 6.3837 3rd Qu.: 6.3837 3rd Qu.: 6.3827
GSM674315 GSM674316 GSM674317 GSM674318 GSM674319 GSM674320 GSM674321
Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8400 1st Qu.: 1.8400 1st Qu.: 1.8347 1st Qu.: 1.8445 1st Qu.: 1.8452 1st Qu.: 1.8477 1st Qu.: 1.8337
Median : 3.1523 Median : 3.1586 Median : 3.1516 Median : 3.1560 Median : 3.1633 Median : 3.1588 Median : 3.1562
Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616 Mean : 4.2617 Mean : 4.2616
3rd Qu.: 6.3832 3rd Qu.: 6.3832 3rd Qu.: 6.3834 3rd Qu.: 6.3840 3rd Qu.: 6.3832 3rd Qu.: 6.3840 3rd Qu.: 6.3845
GSM674322 GSM674323 GSM674324 GSM674325 GSM674326 GSM674327 GSM674328
Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8473 1st Qu.: 1.8447 1st Qu.: 1.8395 1st Qu.: 1.8443 1st Qu.: 1.8498 1st Qu.: 1.8486 1st Qu.: 1.8455
Median : 3.1586 Median : 3.1543 Median : 3.1536 Median : 3.1604 Median : 3.1522 Median : 3.1578 Median : 3.1534
Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616
3rd Qu.: 6.3832 3rd Qu.: 6.3827 3rd Qu.: 6.3832 3rd Qu.: 6.3846 3rd Qu.: 6.3832 3rd Qu.: 6.3843 3rd Qu.: 6.3825
GSM674329 GSM674330 GSM674331 GSM674332 GSM674333 GSM674334 GSM674335
Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107 Min. : 0.5107
1st Qu.: 1.8502 1st Qu.: 1.8413 1st Qu.: 1.8385 1st Qu.: 1.8357 1st Qu.: 1.8467 1st Qu.: 1.8467 1st Qu.: 1.8326
Median : 3.1559 Median : 3.1512 Median : 3.1504 Median : 3.1516 Median : 3.1629 Median : 3.1591 Median : 3.1628
Mean : 4.2616 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2617 Mean : 4.2616
3rd Qu.: 6.3821 3rd Qu.: 6.3830 3rd Qu.: 6.3837 3rd Qu.: 6.3851 3rd Qu.: 6.3830 3rd Qu.: 6.3832 3rd Qu.: 6.3830
GSM674344 GSM674345 GSM674346 GSM674347 GSM674348 GSM674349 GSM674350
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5757 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8533 1st Qu.: 1.8561 1st Qu.: 1.8517 1st Qu.: 1.8557 1st Qu.: 1.8578 1st Qu.: 1.8534 1st Qu.: 1.8498
Median : 3.1006 Median : 3.1004 Median : 3.0993 Median : 3.1058 Median : 3.1034 Median : 3.0996 Median : 3.1019
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3895 3rd Qu.: 6.3890 3rd Qu.: 6.3892 3rd Qu.: 6.3898 3rd Qu.: 6.3893 3rd Qu.: 6.3884 3rd Qu.: 6.3886
GSM674351 GSM674352 GSM674353 GSM674354 GSM674355 GSM674356 GSM674357
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5757 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8519 1st Qu.: 1.8540 1st Qu.: 1.8535 1st Qu.: 1.8558 1st Qu.: 1.8567 1st Qu.: 1.8522 1st Qu.: 1.8506
Median : 3.0965 Median : 3.1025 Median : 3.0976 Median : 3.0954 Median : 3.0997 Median : 3.0985 Median : 3.1046
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3894 3rd Qu.: 6.3881 3rd Qu.: 6.3879 3rd Qu.: 6.3890 3rd Qu.: 6.3892 3rd Qu.: 6.3894 3rd Qu.: 6.3893
GSM674358 GSM674359 GSM674360 GSM674361 GSM674362 GSM674363 GSM674364
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8575 1st Qu.: 1.8518 1st Qu.: 1.8497 1st Qu.: 1.8591 1st Qu.: 1.8515 1st Qu.: 1.8594 1st Qu.: 1.8580
Median : 3.1057 Median : 3.0993 Median : 3.1057 Median : 3.0975 Median : 3.1059 Median : 3.1034 Median : 3.1044
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3895 3rd Qu.: 6.3891 3rd Qu.: 6.3895 3rd Qu.: 6.3893 3rd Qu.: 6.3884 3rd Qu.: 6.3895 3rd Qu.: 6.3906
GSM674365 GSM674366 GSM674367 GSM674368 GSM674369 GSM674370 GSM674371
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8563 1st Qu.: 1.8538 1st Qu.: 1.8574 1st Qu.: 1.8578 1st Qu.: 1.8567 1st Qu.: 1.8547 1st Qu.: 1.8579
Median : 3.1001 Median : 3.0991 Median : 3.0979 Median : 3.0993 Median : 3.0945 Median : 3.1006 Median : 3.0996
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3890 3rd Qu.: 6.3897 3rd Qu.: 6.3893 3rd Qu.: 6.3894 3rd Qu.: 6.3895 3rd Qu.: 6.3893 3rd Qu.: 6.3892
GSM674372 GSM674373 GSM674374 GSM674375 GSM674376 GSM674377 GSM674378
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8598 1st Qu.: 1.8518 1st Qu.: 1.8523 1st Qu.: 1.8589 1st Qu.: 1.8586 1st Qu.: 1.8578 1st Qu.: 1.8479
Median : 3.1118 Median : 3.1015 Median : 3.1006 Median : 3.0980 Median : 3.1038 Median : 3.1017 Median : 3.1017
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3893 3rd Qu.: 6.3890 3rd Qu.: 6.3894 3rd Qu.: 6.3886 3rd Qu.: 6.3884 3rd Qu.: 6.3895 3rd Qu.: 6.3895
GSM674379 GSM674380 GSM674381 GSM674382 GSM674383 GSM674384 GSM674385
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8578 1st Qu.: 1.8595 1st Qu.: 1.8497 1st Qu.: 1.8546 1st Qu.: 1.8561 1st Qu.: 1.8506 1st Qu.: 1.8557
Median : 3.0977 Median : 3.0997 Median : 3.1013 Median : 3.1061 Median : 3.1017 Median : 3.1025 Median : 3.1071
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3894 3rd Qu.: 6.3881 3rd Qu.: 6.3884 3rd Qu.: 6.3890 3rd Qu.: 6.3895 3rd Qu.: 6.3893 3rd Qu.: 6.3894
GSM674386 GSM674387 GSM674388 GSM674389 GSM674390 GSM674391 GSM674392
Min. : 0.5477 Min. : 0.5477 Min. : 0.5757 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8557 1st Qu.: 1.8479 1st Qu.: 1.8541 1st Qu.: 1.8595 1st Qu.: 1.8512 1st Qu.: 1.8519 1st Qu.: 1.8545
Median : 3.0951 Median : 3.1034 Median : 3.1062 Median : 3.0917 Median : 3.1006 Median : 3.0997 Median : 3.1015
Mean : 4.2541 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3879 3rd Qu.: 6.3894 3rd Qu.: 6.3893 3rd Qu.: 6.3888 3rd Qu.: 6.3892 3rd Qu.: 6.3886 3rd Qu.: 6.3890
GSM674393 GSM674394 GSM674395 GSM674396 GSM674397 GSM674398 GSM674399
Min. : 0.5477 Min. : 0.5757 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8554 1st Qu.: 1.8505 1st Qu.: 1.8467 1st Qu.: 1.8517 1st Qu.: 1.8534 1st Qu.: 1.8513 1st Qu.: 1.8620
Median : 3.1066 Median : 3.0967 Median : 3.1019 Median : 3.0929 Median : 3.1057 Median : 3.1038 Median : 3.1092
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3895 3rd Qu.: 6.3895 3rd Qu.: 6.3881 3rd Qu.: 6.3895 3rd Qu.: 6.3890 3rd Qu.: 6.3895 3rd Qu.: 6.3900
GSM674400 GSM674401 GSM674402 GSM674403 GSM674404 GSM674405 GSM674406
Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477 Min. : 0.5477
1st Qu.: 1.8481 1st Qu.: 1.8612 1st Qu.: 1.8486 1st Qu.: 1.8523 1st Qu.: 1.8530 1st Qu.: 1.8601 1st Qu.: 1.8594
Median : 3.0915 Median : 3.0999 Median : 3.1074 Median : 3.1106 Median : 3.1046 Median : 3.1061 Median : 3.0948
Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540 Mean : 4.2540
3rd Qu.: 6.3890 3rd Qu.: 6.3871 3rd Qu.: 6.3890 3rd Qu.: 6.3898 3rd Qu.: 6.3894 3rd Qu.: 6.3881 3rd Qu.: 6.3884
GSM674407
Min. : 0.5477
1st Qu.: 1.8518
Median : 3.1019
Mean : 4.2540
3rd Qu.: 6.3895
[ reached getOption("max.print") -- omitted 1 row ]If this output we clearly see that the values go beyond 16, so we will need to perform a log2 transformation. A boxplot can also be generated to see if the data have been normalised. If so, the distributions of each sample should be highly similar.
exprs(gsePS) <- log2(exprs(gsePS))
boxplot(exprs(gsePS),outline=FALSE)
exprs(gseAS) <- log2(exprs(gseAS))
boxplot(exprs(gseAS),outline=FALSE)
Inspect the clinical variables. Data submitted to GEO contain sample labels assigned by the experimenters, and some information about the processing protocol. All these data can be extracted by the pData function.
For your own data, you will have to decide which columns will be useful in the analysis. This will include the column giving the main comparison(s) of interest and any potential confounding factors. In this particular data-set it looks like source_name_ch1 and characteristics_ch1.1.
We can use the select function from dplyr to display just these columns of interest. At this stage it will also be useful to rename the columns to something more convenient using the rename function.
library (dplyr)
Attaching package: ‘dplyr’
The following object is masked from ‘package:Biobase’:
combine
The following objects are masked from ‘package:BiocGenerics’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, unionsampleInfoPS <- pData(gsePS)
print(sampleInfoPS)
sampleInfoAS <- pData(gseAS)
print(sampleInfoAS)## source_name_ch1 and characteristics_ch1.1 seem to contain factors we might need for the analysis. Let's pick just those columns
sampleInfoPS <- select(sampleInfoPS, source_name_ch1, characteristics_ch1.1)
sampleInfoAS <- select(sampleInfoAS, source_name_ch1, characteristics_ch1.1)
## Optionally, rename to more convenient column names
sampleInfoPS <- rename(sampleInfoPS,group = source_name_ch1, patient=characteristics_ch1.1)
sampleInfoAS <- rename(sampleInfoAS,group = source_name_ch1, patient=characteristics_ch1.1)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